Literature DB >> 31980345

Viewing Nuclear Architecture through the Eyes of Nocturnal Mammals.

Yana Feodorova1, Martin Falk2, Leonid A Mirny3, Irina Solovei4.   

Abstract

The cell nucleus is a remarkably well-organized organelle with membraneless but distinct compartments of various functions. The largest of them, euchromatin and heterochromatin, are spatially segregated in such a way that the transcriptionally active genome occupies the nuclear interior, whereas silent genomic loci are preferentially associated with the nuclear envelope. This rule is broken by rod photoreceptor cells of nocturnal mammals, in which the two major compartments have inverted positions. The inversion and dense compaction of heterochromatin converts these nuclei into microlenses that focus light and facilitate nocturnal vision. As is often the case in biology, when a mutation helps to understand normal processes and structures, inverted nuclei have served as a tool to unravel general principles of nuclear organization, including mechanisms of heterochromatin tethering to the nuclear envelope, autonomous behavior of small genomic segments, and euchromatin-heterochromatin segregation.
Copyright © 2019 Elsevier Ltd. All rights reserved.

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Year:  2020        PMID: 31980345      PMCID: PMC7293902          DOI: 10.1016/j.tcb.2019.12.008

Source DB:  PubMed          Journal:  Trends Cell Biol        ISSN: 0962-8924            Impact factor:   20.808


  104 in total

1.  Step-wise methylation of histone H3K9 positions heterochromatin at the nuclear periphery.

Authors:  Benjamin D Towbin; Cristina González-Aguilera; Ragna Sack; Dimos Gaidatzis; Véronique Kalck; Peter Meister; Peter Askjaer; Susan M Gasser
Journal:  Cell       Date:  2012-08-31       Impact factor: 41.582

2.  Clustering of mammalian Hox genes with other H3K27me3 targets within an active nuclear domain.

Authors:  Maxence Vieux-Rochas; Pierre J Fabre; Marion Leleu; Denis Duboule; Daan Noordermeer
Journal:  Proc Natl Acad Sci U S A       Date:  2015-03-30       Impact factor: 11.205

3.  Transcription Factors Activate Genes through the Phase-Separation Capacity of Their Activation Domains.

Authors:  Ann Boija; Isaac A Klein; Benjamin R Sabari; Alessandra Dall'Agnese; Eliot L Coffey; Alicia V Zamudio; Charles H Li; Krishna Shrinivas; John C Manteiga; Nancy M Hannett; Brian J Abraham; Lena K Afeyan; Yang E Guo; Jenna K Rimel; Charli B Fant; Jurian Schuijers; Tong Ihn Lee; Dylan J Taatjes; Richard A Young
Journal:  Cell       Date:  2018-11-15       Impact factor: 41.582

4.  Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Authors:  Erez Lieberman-Aiden; Nynke L van Berkum; Louise Williams; Maxim Imakaev; Tobias Ragoczy; Agnes Telling; Ido Amit; Bryan R Lajoie; Peter J Sabo; Michael O Dorschner; Richard Sandstrom; Bradley Bernstein; M A Bender; Mark Groudine; Andreas Gnirke; John Stamatoyannopoulos; Leonid A Mirny; Eric S Lander; Job Dekker
Journal:  Science       Date:  2009-10-09       Impact factor: 47.728

5.  Chromatin Organization by Repetitive Elements (CORE): A Genomic Principle for the Higher-Order Structure of Chromosomes.

Authors:  Shao-Jun Tang
Journal:  Genes (Basel)       Date:  2011-08-02       Impact factor: 4.096

6.  Small chromosomal regions position themselves autonomously according to their chromatin class.

Authors:  Harmen J G van de Werken; Josien C Haan; Yana Feodorova; Dominika Bijos; An Weuts; Koen Theunis; Sjoerd J B Holwerda; Wouter Meuleman; Ludo Pagie; Katharina Thanisch; Parveen Kumar; Heinrich Leonhardt; Peter Marynen; Bas van Steensel; Thierry Voet; Wouter de Laat; Irina Solovei; Boris Joffe
Journal:  Genome Res       Date:  2017-03-24       Impact factor: 9.043

7.  Multiscale 3D Genome Rewiring during Mouse Neural Development.

Authors:  Boyan Bonev; Netta Mendelson Cohen; Quentin Szabo; Lauriane Fritsch; Giorgio L Papadopoulos; Yaniv Lubling; Xiaole Xu; Xiaodan Lv; Jean-Philippe Hugnot; Amos Tanay; Giacomo Cavalli
Journal:  Cell       Date:  2017-10-19       Impact factor: 41.582

8.  Nuclear pore density controls heterochromatin reorganization during senescence.

Authors:  Charlene Boumendil; Priya Hari; Karl C F Olsen; Juan Carlos Acosta; Wendy A Bickmore
Journal:  Genes Dev       Date:  2019-01-28       Impact factor: 11.361

9.  Pol II phosphorylation regulates a switch between transcriptional and splicing condensates.

Authors:  Yang Eric Guo; John C Manteiga; Jonathan E Henninger; Benjamin R Sabari; Alessandra Dall'Agnese; Nancy M Hannett; Jan-Hendrik Spille; Lena K Afeyan; Alicia V Zamudio; Krishna Shrinivas; Brian J Abraham; Ann Boija; Tim-Michael Decker; Jenna K Rimel; Charli B Fant; Tong Ihn Lee; Ibrahim I Cisse; Phillip A Sharp; Dylan J Taatjes; Richard A Young
Journal:  Nature       Date:  2019-08-07       Impact factor: 49.962

10.  Structure and dynamics of interphase chromosomes.

Authors:  Angelo Rosa; Ralf Everaers
Journal:  PLoS Comput Biol       Date:  2008-08-22       Impact factor: 4.475

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  13 in total

Review 1.  Regulation and dysregulation of spatial chromatin structure in the central nervous system.

Authors:  Yuki Fujita
Journal:  Anat Sci Int       Date:  2021-01-03       Impact factor: 1.741

Review 2.  The relationship between genome structure and function.

Authors:  A Marieke Oudelaar; Douglas R Higgs
Journal:  Nat Rev Genet       Date:  2020-11-24       Impact factor: 53.242

Review 3.  RASER-FISH: non-denaturing fluorescence in situ hybridization for preservation of three-dimensional interphase chromatin structure.

Authors:  Jill M Brown; Sara De Ornellas; Eva Parisi; Lothar Schermelleh; Veronica J Buckle
Journal:  Nat Protoc       Date:  2022-04-04       Impact factor: 13.491

4.  The interplay of chromatin phase separation and lamina interactions in nuclear organization.

Authors:  Rabia Laghmach; Michele Di Pierro; Davit A Potoyan
Journal:  Biophys J       Date:  2021-10-13       Impact factor: 4.033

5.  Impact of chromosomal organization on epigenetic drift and domain stability revealed by physics-based simulations.

Authors:  Joseph G Wakim; Sarah H Sandholtz; Andrew J Spakowitz
Journal:  Biophys J       Date:  2021-10-21       Impact factor: 4.033

6.  Spatial organization of transcribed eukaryotic genes.

Authors:  Johannes Ribisel; Simon Ullrich; Susanne Leidescher; Yana Feodorova; Erica Hildebrand; Alexandra Galitsyna; Sebastian Bultmann; Stephanie Link; Katharina Thanisch; Christopher Mulholland; Job Dekker; Heinrich Leonhardt; Leonid Mirny; Irina Solovei
Journal:  Nat Cell Biol       Date:  2022-02-17       Impact factor: 28.213

7.  A new emu genome illuminates the evolution of genome configuration and nuclear architecture of avian chromosomes.

Authors:  Jing Liu; Zongji Wang; Jing Li; Luohao Xu; Jiaqi Liu; Shaohong Feng; Chunxue Guo; Shengchan Chen; Zhanjun Ren; Jinpeng Rao; Kai Wei; Yuezhou Chen; Erich D Jarvis; Guojie Zhang; Qi Zhou
Journal:  Genome Res       Date:  2021-01-06       Impact factor: 9.043

Review 8.  Nuclear organization and regulation of the differentiated state.

Authors:  Eliya Bitman-Lotan; Amir Orian
Journal:  Cell Mol Life Sci       Date:  2021-01-28       Impact factor: 9.261

9.  TAD cliques predict key features of chromatin organization.

Authors:  Tharvesh M Liyakat Ali; Annaël Brunet; Philippe Collas; Jonas Paulsen
Journal:  BMC Genomics       Date:  2021-07-03       Impact factor: 3.969

10.  Differences in the Response to DNA Double-Strand Breaks between Rod Photoreceptors of Rodents, Pigs, and Humans.

Authors:  Florian Frohns; Antonia Frohns; Johanna Kramer; Katharina Meurer; Carla Rohrer-Bley; Irina Solovei; David Hicks; Paul G Layer; Markus Löbrich
Journal:  Cells       Date:  2020-04-12       Impact factor: 6.600

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